CoV-GLUE Mutation

CoV-GLUE Mutation: ORF = ORF3a : CodonNum = 41

Details of the codons used for the mutation across all lineages (CodonProp is the proportion each codon is used for this AA mutation):

ORF	CodonNum	Mut	ORF1abMut	MutType	RefCodon	MutCodon	AACount	CodonCount	CodonProp	Genome Position
ORF3a	41	L41F		nonsyn	Ctc	Ttc	11199	11196	0.999732	25513-25515
ORF3a	41	L41F		nonsyn	CtC	TtT	11199	3	0.000267881	25513-25515
ORF3a	41	L41L		syn	ctC	ctT	2553	2464	0.965139	25513-25515
ORF3a	41	L41L		syn	ctC	ctA	2553	86	0.0336859	25513-25515
ORF3a	41	L41L		syn	ctC	ctG	2553	3	0.00117509	25513-25515
ORF3a	41	L41R		nonsyn	cTc	cGc	1173	1172	0.999147	25513-25515
ORF3a	41	L41R		nonsyn	cTC	cGT	1173	1	0.000852515	25513-25515
ORF3a	41	L41del		del	CTC	---	860	860	1	25513-25515
ORF3a	41	L41P		nonsyn	cTc	cCc	709	708	0.99859	25513-25515
ORF3a	41	L41P		nonsyn	cTC	cCT	709	1	0.00141044	25513-25515
ORF3a	41	L41I		nonsyn	Ctc	Atc	628	627	0.998408	25513-25515
ORF3a	41	L41I		nonsyn	CtC	AtT	628	1	0.00159236	25513-25515
ORF3a	41	L41H		nonsyn	cTc	cAc	137	137	1	25513-25515
ORF3a	41	L41V		nonsyn	Ctc	Gtc	125	125	1	25513-25515
ORF3a	41	L41del1		del	Ctc	-tc	4	2	0.5	25513-25515
ORF3a	41	L41del1		del	ctC	ct-	4	1	0.25	25513-25515
ORF3a	41	L41del1		del	cTc	c-c	4	1	0.25	25513-25515
ORF3a	41	L41S		nonsyn	CTc	TCc	2	2	1	25513-25515
ORF3a	41	L41Q		nonsyn	cTC	cAA	1	1	1	25513-25515
ORF3a	41	L41del2		del	cTC	c--	1	1	1	25513-25515

Details of the mutation no within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):

ORF	CodonNum	Mut	RefCodon	MutCodon	CodonCount	AACount	Lineage	LineageCodonProp
ORF3a	41	L41F	Ctc	Ttc	11196	11199	All	0.002141
ORF3a	41	L41F	CtC	TtT	3	11199	All	0.000001
ORF3a	41	L41L	ctC	ctT	2464	2553	All	0.000471
ORF3a	41	L41L	ctC	ctA	86	2553	All	0.000016
ORF3a	41	L41L	ctC	ctG	3	2553	All	0.000001
ORF3a	41	L41F	Ctc	Ttc	2185	2187	AY.98.1	0.105821
ORF3a	41	L41F	CtC	TtT	2	2187	AY.98.1	0.000097
ORF3a	41	L41F	Ctc	Ttc	1875	1875	AY.4	0.002918
ORF3a	41	L41F	Ctc	Ttc	1430	1430	B.1.1.7	0.00128
ORF3a	41	L41R	cTc	cGc	1172	1173	All	0.000224
ORF3a	41	L41R	cTC	cGT	1	1173	All	0
ORF3a	41	L41del	CTC	---	860	860	All	0.000164
ORF3a	41	L41P	cTc	cCc	708	709	All	0.000135
ORF3a	41	L41P	cTC	cCT	1	709	All	0
ORF3a	41	L41L	ctC	ctT	656	656	B.1.1.7	0.000587
ORF3a	41	L41I	Ctc	Atc	627	628	All	0.00012
ORF3a	41	L41I	CtC	AtT	1	628	All	0
ORF3a	41	L41R	cTc	cGc	585	586	AY.121	0.079161
ORF3a	41	L41R	cTC	cGT	1	586	AY.121	0.000135
ORF3a	41	L41F	Ctc	Ttc	573	574	B.1.617.2	0.002158
ORF3a	41	L41F	CtC	TtT	1	574	B.1.617.2	0.000004
ORF3a	41	L41F	Ctc	Ttc	543	543	AY.43	0.002406
ORF3a	41	L41F	Ctc	Ttc	511	511	B.1.628	0.180056
ORF3a	41	L41L	ctC	ctT	440	440	AY.6	0.018097
ORF3a	41	L41F	Ctc	Ttc	395	395	B.1.2	0.003478
ORF3a	41	L41F	Ctc	Ttc	340	340	B.1.177	0.004477
ORF3a	41	L41R	cTc	cGc	338	338	B.1.617.2	0.001273
ORF3a	41	L41L	ctC	ctT	335	335	AY.43	0.001484
ORF3a	41	L41F	Ctc	Ttc	267	267	AY.102	0.007079
ORF3a	41	L41F	Ctc	Ttc	235	235	AY.44	0.00143
ORF3a	41	L41F	Ctc	Ttc	202	202	P.1	0.003182
ORF3a	41	L41del	CTC	---	192	192	AY.26	0.005436
ORF3a	41	L41P	cTc	cCc	182	182	AY.113	0.025915
ORF3a	41	L41F	Ctc	Ttc	174	174	AY.39	0.0043
ORF3a	41	L41I	Ctc	Atc	173	174	AY.44	0.001053
ORF3a	41	L41I	CtC	AtT	1	174	AY.44	0.000006
ORF3a	41	L41del	CTC	---	153	153	B.1.630	0.801047
ORF3a	41	L41F	Ctc	Ttc	147	147	AY.120	0.005465
ORF3a	41	L41H	cTc	cAc	137	137	All	0.000026
ORF3a	41	L41F	Ctc	Ttc	129	129	B.1	0.001182
ORF3a	41	L41L	ctC	ctT	128	128	P.1	0.002017
ORF3a	41	L41L	ctC	ctT	126	127	B.1.617.2	0.000474
ORF3a	41	L41L	ctC	ctA	1	127	B.1.617.2	0.000004
ORF3a	41	L41F	Ctc	Ttc	126	126	B.1.1	0.002286
ORF3a	41	L41V	Ctc	Gtc	125	125	All	0.000024
ORF3a	41	L41R	cTc	cGc	114	114	AY.75	0.006387
ORF3a	41	L41F	Ctc	Ttc	100	100	B.1.177.27	0.943396
ORF3a	41	L41L	ctC	ctT	97	98	B.1.2	0.000854
ORF3a	41	L41L	ctC	ctG	1	98	B.1.2	0.000009
ORF3a	41	L41F	Ctc	Ttc	93	93	B.1.1.141	0.187123
ORF3a	41	L41F	Ctc	Ttc	91	91	AY.25	0.000547
ORF3a	41	L41F	Ctc	Ttc	88	88	AY.103	0.000546
ORF3a	41	L41F	Ctc	Ttc	86	86	AY.3	0.000855
ORF3a	41	L41I	Ctc	Atc	86	86	AY.92	0.024706
ORF3a	41	L41F	Ctc	Ttc	85	85	B.1.258.17	0.008838
ORF3a	41	L41I	Ctc	Atc	84	84	B.1.1.7	0.000075
ORF3a	41	L41P	cTc	cCc	72	72	B.1.1.7	0.000064
ORF3a	41	L41L	ctC	ctT	70	70	AY.120.1	0.022472
ORF3a	41	L41F	Ctc	Ttc	69	69	AY.29	0.001088
ORF3a	41	L41del	CTC	---	69	69	AY.43	0.000306
ORF3a	41	L41L	ctC	ctT	64	67	AY.4	0.0001
ORF3a	41	L41L	ctC	ctA	3	67	AY.4	0.000005
ORF3a	41	L41F	Ctc	Ttc	65	65	B.1.1.284	0.006981
ORF3a	41	L41L	ctC	ctT	50	64	AY.44	0.000304
ORF3a	41	L41L	ctC	ctA	14	64	AY.44	0.000085
ORF3a	41	L41F	Ctc	Ttc	63	63	AY.75	0.003529
ORF3a	41	L41del	CTC	---	63	63	B.1.1.7	0.000056
ORF3a	41	L41F	Ctc	Ttc	63	63	B.1.177.44	0.032693
ORF3a	41	L41F	Ctc	Ttc	57	57	B.1.563	0.966102
ORF3a	41	L41L	ctC	ctT	55	55	B.1.429	0.001294
ORF3a	41	L41del	CTC	---	54	54	B.1.177.82	0.025776
ORF3a	41	L41F	Ctc	Ttc	53	53	A.2.5	0.026447
ORF3a	41	L41I	Ctc	Atc	49	49	AY.84	0.021435
ORF3a	41	L41V	Ctc	Gtc	48	48	B.1.351	0.001427
ORF3a	41	L41P	cTc	cCc	46	46	B.1.177.58	0.061252
ORF3a	41	L41F	Ctc	Ttc	42	42	B.1.1.222	0.008568
ORF3a	41	L41F	Ctc	Ttc	40	40	AY.119	0.001412
ORF3a	41	L41P	cTc	cCc	38	38	AY.4	0.000059
ORF3a	41	L41L	ctC	ctT	37	37	B.1.1.222	0.007548
ORF3a	41	L41L	ctC	ctT	37	37	B.1.177	0.000487
ORF3a	41	L41del	CTC	---	36	36	B.1.177	0.000474
ORF3a	41	L41I	Ctc	Atc	36	36	B.1.617.2	0.000136
ORF3a	41	L41R	cTc	cGc	34	34	AY.25	0.000205
ORF3a	41	L41F	Ctc	Ttc	34	34	AY.92	0.009767
ORF3a	41	L41F	Ctc	Ttc	34	34	B.1.526	0.000799
ORF3a	41	L41L	ctC	ctA	32	32	B.1.177.12	0.004854
ORF3a	41	L41P	cTc	cCc	32	32	B.1.617.2	0.00012
ORF3a	41	L41del	CTC	---	30	30	AY.4	0.000047
ORF3a	41	L41F	Ctc	Ttc	30	30	AY.5	0.000619
ORF3a	41	L41I	Ctc	Atc	29	29	AY.25	0.000174
ORF3a	41	L41F	Ctc	Ttc	29	29	AY.26	0.000821
ORF3a	41	L41L	ctC	ctT	29	29	Q.1	0.003663
ORF3a	41	L41F	Ctc	Ttc	28	28	AY.42	0.001126
ORF3a	41	L41H	cTc	cAc	27	27	B.1.1.7	0.000024
ORF3a	41	L41F	Ctc	Ttc	27	27	B.1.621	0.00239
ORF3a	41	L41P	cTc	cCc	26	26	AY.3	0.000259
ORF3a	41	L41I	Ctc	Atc	26	26	AY.4	0.00004
ORF3a	41	L41del	CTC	---	26	26	B.1.617.2	0.000098
ORF3a	41	L41L	ctC	ctT	25	25	B.1.1	0.000454
ORF3a	41	L41P	cTc	cCc	23	23	AY.6	0.000946
ORF3a	41	L41del	CTC	---	23	23	B.1.1	0.000417
ORF3a	41	L41F	Ctc	Ttc	22	22	AY.68	0.006022
ORF3a	41	L41P	cTc	cCc	21	21	AY.103	0.00013
ORF3a	41	L41del	CTC	---	21	21	AY.25	0.000126
ORF3a	41	L41I	Ctc	Atc	21	21	AY.3.1	0.00179
ORF3a	41	L41F	Ctc	Ttc	20	20	B.1.177.81	0.003786
ORF3a	41	L41F	Ctc	Ttc	20	20	B.1.351	0.000595
ORF3a	41	L41F	Ctc	Ttc	20	20	P.1.17	0.003235
ORF3a	41	L41F	Ctc	Ttc	19	19	AY.4.2	0.000412
ORF3a	41	L41L	ctC	ctT	13	19	B.1	0.000119
ORF3a	41	L41L	ctC	ctA	6	19	B.1	0.000055
ORF3a	41	L41F	Ctc	Ttc	19	19	B.1.234	0.002507
ORF3a	41	L41F	Ctc	Ttc	19	19	B.1.565	0.015397
ORF3a	41	L41P	cTc	cCc	18	18	AY.33	0.001202
ORF3a	41	L41H	cTc	cAc	18	18	AY.46	0.001873
ORF3a	41	L41P	cTc	cCc	17	17	AY.20	0.000661
ORF3a	41	L41R	cTc	cGc	17	17	AY.39	0.00042
ORF3a	41	L41P	cTc	cCc	17	17	B.1.2	0.00015
ORF3a	41	L41F	Ctc	Ttc	17	17	B.1.525	0.001924
ORF3a	41	L41P	cTc	cCc	16	16	AY.25	0.000096
ORF3a	41	L41F	Ctc	Ttc	16	16	AY.47	0.000498
ORF3a	41	L41L	ctC	ctT	9	15	AY.103	0.000056
ORF3a	41	L41L	ctC	ctA	6	15	AY.103	0.000037
ORF3a	41	L41F	Ctc	Ttc	15	15	AY.20	0.000583
ORF3a	41	L41I	Ctc	Atc	15	15	B.1.177.81	0.00284
ORF3a	41	L41L	ctC	ctA	15	15	B.1.36.29	0.00776
ORF3a	41	L41V	Ctc	Gtc	14	14	AY.103	0.000087
ORF3a	41	L41P	cTc	cCc	14	14	AY.61	0.001467
ORF3a	41	L41F	Ctc	Ttc	14	14	AY.98	0.001106
ORF3a	41	L41F	Ctc	Ttc	14	14	B.1.177.21	0.001071
ORF3a	41	L41V	Ctc	Gtc	14	14	B.1.617.2	0.000053
ORF3a	41	L41H	cTc	cAc	14	14	B.1.617.2	0.000053
ORF3a	41	L41del	CTC	---	14	14	P.1	0.000221
ORF3a	41	L41F	Ctc	Ttc	13	13	AY.39.1	0.000515
ORF3a	41	L41del	CTC	---	13	13	AY.98.1	0.00063
ORF3a	41	L41F	Ctc	Ttc	13	13	B.1.258	0.000865
ORF3a	41	L41F	Ctc	Ttc	13	13	B.1.258.11	0.005153
ORF3a	41	L41F	Ctc	Ttc	13	13	B.1.36	0.001897
ORF3a	41	L41L	ctC	ctT	11	12	AY.102	0.000292
ORF3a	41	L41L	ctC	ctA	1	12	AY.102	0.000027
ORF3a	41	L41F	Ctc	Ttc	12	12	AY.107	0.005592
ORF3a	41	L41L	ctC	ctT	12	12	AY.34	0.001164
ORF3a	41	L41V	Ctc	Gtc	12	12	AY.44	0.000073
ORF3a	41	L41F	Ctc	Ttc	12	12	AY.54	0.001144
ORF3a	41	L41P	cTc	cCc	12	12	AY.75	0.000672
ORF3a	41	L41F	Ctc	Ttc	12	12	AY.95	0.009132
ORF3a	41	L41P	cTc	cCc	12	12	B.1.351	0.000357
ORF3a	41	L41P	cTc	cCc	12	12	B.1.429	0.000282
ORF3a	41	L41F	Ctc	Ttc	12	12	B.1.596	0.001046
ORF3a	41	L41del	CTC	---	11	11	AY.3	0.000109
ORF3a	41	L41F	Ctc	Ttc	11	11	AY.45	0.001339
ORF3a	41	L41F	Ctc	Ttc	11	11	B.1.1.207	0.013002
ORF3a	41	L41F	Ctc	Ttc	11	11	B.1.243	0.000765
ORF3a	41	L41F	Ctc	Ttc	11	11	B.1.311	0.00302
ORF3a	41	L41I	Ctc	Atc	11	11	B.1.474	0.020913
ORF3a	41	L41F	Ctc	Ttc	11	11	B.1.582	0.005397
ORF3a	41	L41F	Ctc	Ttc	11	11	Q.2	0.006748
ORF3a	41	L41H	cTc	cAc	10	10	AY.100	0.00046
ORF3a	41	L41I	Ctc	Atc	10	10	AY.20	0.000389
ORF3a	41	L41I	Ctc	Atc	10	10	AY.43	0.000044
ORF3a	41	L41L	ctC	ctT	10	10	AY.88	0.008842
ORF3a	41	L41R	cTc	cGc	10	10	AY.98	0.00079
ORF3a	41	L41F	Ctc	Ttc	10	10	B.1.1.519	0.000397
ORF3a	41	L41F	Ctc	Ttc	10	10	B.1.160	0.000312
ORF3a	41	L41L	ctC	ctT	10	10	B.1.351	0.000297
ORF3a	41	L41P	cTc	cCc	9	9	AY.26	0.000255
ORF3a	41	L41L	ctC	ctT	9	9	AY.27	0.000582
ORF3a	41	L41H	cTc	cAc	9	9	AY.43	0.00004
ORF3a	41	L41F	Ctc	Ttc	9	9	AY.46.2	0.005718
ORF3a	41	L41L	ctC	ctT	8	9	AY.5	0.000165
ORF3a	41	L41L	ctC	ctA	1	9	AY.5	0.000021
ORF3a	41	L41P	cTc	cCc	9	9	AY.9	0.000608
ORF3a	41	L41P	cTc	cCc	9	9	B.1	0.000082
ORF3a	41	L41I	Ctc	Atc	9	9	B.1	0.000082
ORF3a	41	L41L	ctC	ctT	9	9	B.1.1.294	0.011392
ORF3a	41	L41del	CTC	---	9	9	B.1.258	0.000599
ORF3a	41	L41F	Ctc	Ttc	9	9	C.37	0.001045
ORF3a	41	L41P	cTc	cCc	9	9	P.1	0.000142
ORF3a	41	L41del	CTC	---	8	8	AY.103	0.00005
ORF3a	41	L41L	ctC	ctT	8	8	AY.111	0.001465
ORF3a	41	L41R	cTc	cGc	8	8	AY.117	0.000676
ORF3a	41	L41V	Ctc	Gtc	8	8	AY.25	0.000048
ORF3a	41	L41R	cTc	cGc	8	8	AY.43	0.000035
ORF3a	41	L41H	cTc	cAc	8	8	AY.46.1	0.008214
ORF3a	41	L41F	Ctc	Ttc	8	8	AY.61	0.000838
ORF3a	41	L41F	Ctc	Ttc	8	8	B.1.1.214	0.000444
ORF3a	41	L41P	cTc	cCc	8	8	B.1.177	0.000105
ORF3a	41	L41L	ctC	ctT	8	8	B.1.177.44	0.004152
ORF3a	41	L41F	Ctc	Ttc	8	8	B.1.429	0.000188
ORF3a	41	L41L	ctC	ctT	8	8	B.1.596	0.000697
ORF3a	41	L41I	Ctc	Atc	7	7	A.1	0.001973
ORF3a	41	L41L	ctC	ctT	7	7	A.2.5	0.003493
ORF3a	41	L41R	cTc	cGc	7	7	AY.103	0.000043
ORF3a	41	L41L	ctC	ctT	7	7	AY.110	0.000789
ORF3a	41	L41F	Ctc	Ttc	7	7	AY.113	0.000997
ORF3a	41	L41L	ctC	ctT	7	7	AY.25	0.000042
ORF3a	41	L41F	Ctc	Ttc	7	7	AY.33	0.000467
ORF3a	41	L41P	cTc	cCc	7	7	AY.39	0.000173
ORF3a	41	L41del	CTC	---	7	7	AY.39	0.000173
ORF3a	41	L41V	Ctc	Gtc	7	7	AY.4	0.000011
ORF3a	41	L41L	ctC	ctT	7	7	AY.45	0.000852
ORF3a	41	L41F	Ctc	Ttc	7	7	AY.5.3	0.002362
ORF3a	41	L41L	ctC	ctT	7	7	AY.5.4	0.001937
ORF3a	41	L41F	Ctc	Ttc	7	7	AY.7	0.001372
ORF3a	41	L41L	ctC	ctT	7	7	B.1.160	0.000218
ORF3a	41	L41F	Ctc	Ttc	7	7	B.1.177.86	0.001284
ORF3a	41	L41I	Ctc	Atc	7	7	B.1.2	0.000062
ORF3a	41	L41F	Ctc	Ttc	7	7	B.1.36.35	0.018229
ORF3a	41	L41P	cTc	cCc	7	7	B.1.526	0.000165
ORF3a	41	L41F	Ctc	Ttc	7	7	B.40	0.00255
ORF3a	41	L41F	Ctc	Ttc	7	7	D.2	0.000525
ORF3a	41	L41H	cTc	cAc	6	6	AY.103	0.000037
ORF3a	41	L41L	ctC	ctT	6	6	AY.118	0.000376
ORF3a	41	L41F	Ctc	Ttc	6	6	AY.23	0.000418
ORF3a	41	L41del	CTC	---	6	6	AY.44	0.000037
ORF3a	41	L41F	Ctc	Ttc	6	6	AY.9.2	0.00022
ORF3a	41	L41L	ctC	ctT	6	6	AY.92	0.001724
ORF3a	41	L41F	Ctc	Ttc	6	6	B.1.1.187	0.053097
ORF3a	41	L41F	Ctc	Ttc	6	6	B.1.1.311	0.002149
ORF3a	41	L41L	ctC	ctT	6	6	B.1.1.519	0.000238
ORF3a	41	L41F	Ctc	Ttc	6	6	B.1.195	0.030151
ORF3a	41	L41F	Ctc	Ttc	6	6	B.1.36.17	0.002964
ORF3a	41	L41F	Ctc	Ttc	6	6	B.1.427	0.000303
ORF3a	41	L41F	Ctc	Ttc	6	6	B.1.438.1	0.000644
ORF3a	41	L41L	ctC	ctT	6	6	B.1.526	0.000141
ORF3a	41	L41L	ctC	ctT	6	6	B.1.621	0.000531
ORF3a	41	L41F	Ctc	Ttc	6	6	P.1.7	0.001916
ORF3a	41	L41F	Ctc	Ttc	6	6	P.2	0.00112
ORF3a	41	L41F	Ctc	Ttc	6	6	Q.8	0.000989
ORF3a	41	L41F	Ctc	Ttc	5	5	AY.100	0.00023
ORF3a	41	L41F	Ctc	Ttc	5	5	AY.117	0.000423
ORF3a	41	L41F	Ctc	Ttc	5	5	AY.118	0.000313
ORF3a	41	L41P	cTc	cCc	5	5	AY.118	0.000313
ORF3a	41	L41L	ctC	ctT	5	5	AY.29	0.000079
ORF3a	41	L41I	Ctc	Atc	5	5	AY.3	0.00005
ORF3a	41	L41F	Ctc	Ttc	5	5	AY.37	0.00158
ORF3a	41	L41I	Ctc	Atc	5	5	AY.39	0.000124
ORF3a	41	L41H	cTc	cAc	5	5	AY.4	0.000008
ORF3a	41	L41P	cTc	cCc	5	5	AY.43	0.000022
ORF3a	41	L41V	Ctc	Gtc	5	5	AY.43	0.000022
ORF3a	41	L41F	Ctc	Ttc	5	5	AY.46	0.00052
ORF3a	41	L41F	Ctc	Ttc	5	5	AY.84	0.002187
ORF3a	41	L41F	Ctc	Ttc	5	5	AY.90	0.003422
ORF3a	41	L41del	CTC	---	5	5	B.1	0.000046
ORF3a	41	L41del	CTC	---	5	5	B.1.438.1	0.000536
ORF3a	41	L41H	cTc	cAc	5	5	B.1.627	0.010101
ORF3a	41	L41F	Ctc	Ttc	5	5	C.36.2	0.172414
ORF3a	41	L41F	Ctc	Ttc	5	5	P.1.12	0.00242
ORF3a	41	L41F	Ctc	Ttc	5	5	Q.1	0.000632
ORF3a	41	L41F	Ctc	Ttc	4	4	A	0.001548
ORF3a	41	L41F	Ctc	Ttc	4	4	A.27	0.006623
ORF3a	41	L41F	Ctc	Ttc	4	4	AA.1	0.028986
ORF3a	41	L41del1	Ctc	-tc	2	4	All	0
ORF3a	41	L41del1	cTc	c-c	1	4	All	0
ORF3a	41	L41del1	ctC	ct-	1	4	All	0
ORF3a	41	L41F	Ctc	Ttc	4	4	AY.111	0.000733
ORF3a	41	L41F	Ctc	Ttc	4	4	AY.121	0.000541
ORF3a	41	L41L	ctC	ctT	4	4	AY.26	0.000113
ORF3a	41	L41L	ctC	ctT	4	4	AY.4.2	0.000087
ORF3a	41	L41del	CTC	---	4	4	AY.4.2	0.000087
ORF3a	41	L41F	Ctc	Ttc	4	4	AY.4.5	0.00043
ORF3a	41	L41H	cTc	cAc	4	4	AY.44	0.000024
ORF3a	41	L41L	ctC	ctT	4	4	AY.46.6	0.000289
ORF3a	41	L41F	Ctc	Ttc	4	4	AY.46.6	0.000289
ORF3a	41	L41I	Ctc	Atc	4	4	AY.47	0.000124
ORF3a	41	L41R	cTc	cGc	4	4	AY.5	0.000083
ORF3a	41	L41F	Ctc	Ttc	4	4	AY.87	0.003331
ORF3a	41	L41P	cTc	cCc	4	4	B.1.1	0.000073
ORF3a	41	L41del	CTC	---	4	4	B.1.2	0.000035
ORF3a	41	L41F	Ctc	Ttc	4	4	B.1.221	0.000284
ORF3a	41	L41P	cTc	cCc	4	4	B.1.221	0.000284
ORF3a	41	L41F	Ctc	Ttc	4	4	B.1.221.1	0.011628
ORF3a	41	L41I	Ctc	Atc	4	4	B.1.243	0.000278
ORF3a	41	L41L	ctC	ctT	4	4	B.1.243	0.000278
ORF3a	41	L41P	cTc	cCc	4	4	B.1.311	0.001098
ORF3a	41	L41L	ctC	ctA	2	4	B.1.36	0.000292
ORF3a	41	L41L	ctC	ctT	2	4	B.1.36	0.000292
ORF3a	41	L41P	cTc	cCc	4	4	B.1.427	0.000202
ORF3a	41	L41L	ctC	ctT	4	4	P.1.14	0.000191
ORF3a	41	L41F	Ctc	Ttc	4	4	P.1.15	0.000929
ORF3a	41	L41L	ctC	ctT	4	4	P.1.17	0.000647
ORF3a	41	L41del	CTC	---	4	4	P.1.9	0.019231
ORF3a	41	L41F	Ctc	Ttc	3	3	AY.101	0.001471
ORF3a	41	L41F	Ctc	Ttc	3	3	AY.110	0.000338
ORF3a	41	L41F	Ctc	Ttc	3	3	AY.116	0.00086
ORF3a	41	L41H	cTc	cAc	3	3	AY.118	0.000188
ORF3a	41	L41del	CTC	---	3	3	AY.120	0.000112
ORF3a	41	L41L	ctC	ctT	3	3	AY.120	0.000112
ORF3a	41	L41L	ctC	ctT	3	3	AY.14	0.000264
ORF3a	41	L41del	CTC	---	3	3	AY.20	0.000117
ORF3a	41	L41R	cTc	cGc	3	3	AY.23	0.000209
ORF3a	41	L41L	ctC	ctT	2	3	AY.23	0.000139
ORF3a	41	L41L	ctC	ctA	1	3	AY.23	0.00007
ORF3a	41	L41P	cTc	cCc	3	3	AY.24	0.001293
ORF3a	41	L41F	Ctc	Ttc	3	3	AY.27	0.000194
ORF3a	41	L41L	ctC	ctT	3	3	AY.3	0.00003
ORF3a	41	L41L	ctC	ctT	3	3	AY.33	0.0002
ORF3a	41	L41L	ctC	ctT	3	3	AY.39	0.000074
ORF3a	41	L41del	CTC	---	3	3	AY.39.1	0.000119
ORF3a	41	L41F	Ctc	Ttc	3	3	AY.4.4	0.001227
ORF3a	41	L41del	CTC	---	3	3	AY.4.5	0.000322
ORF3a	41	L41del	CTC	---	3	3	AY.40	0.002893
ORF3a	41	L41P	cTc	cCc	3	3	AY.42	0.000121
ORF3a	41	L41R	cTc	cGc	3	3	AY.44	0.000018
ORF3a	41	L41P	cTc	cCc	3	3	AY.44	0.000018
ORF3a	41	L41del	CTC	---	3	3	AY.45	0.000365
ORF3a	41	L41H	cTc	cAc	3	3	AY.62	0.001307
ORF3a	41	L41L	ctC	ctT	3	3	AY.69	0.00056
ORF3a	41	L41F	Ctc	Ttc	3	3	AY.74	0.000347
ORF3a	41	L41F	Ctc	Ttc	3	3	AY.9.1	0.000251
ORF3a	41	L41R	cTc	cGc	3	3	AY.92	0.000862
ORF3a	41	L41F	Ctc	Ttc	3	3	AY.93	0.000819
ORF3a	41	L41del	CTC	---	3	3	AY.98	0.000237
ORF3a	41	L41V	Ctc	Gtc	3	3	B.1.1	0.000054
ORF3a	41	L41F	Ctc	Ttc	3	3	B.1.1.28	0.000934
ORF3a	41	L41F	Ctc	Ttc	3	3	B.1.1.33	0.001263
ORF3a	41	L41F	Ctc	Ttc	3	3	B.1.1.369	0.001339
ORF3a	41	L41F	Ctc	Ttc	3	3	B.1.1.432	0.003797
ORF3a	41	L41H	cTc	cAc	3	3	B.1.1.519	0.000119
ORF3a	41	L41del	CTC	---	3	3	B.1.160.24	0.013274
ORF3a	41	L41F	Ctc	Ttc	3	3	B.1.160.26	0.007264
ORF3a	41	L41F	Ctc	Ttc	3	3	B.1.346	0.003932
ORF3a	41	L41F	Ctc	Ttc	3	3	B.1.411	0.011111
ORF3a	41	L41del	CTC	---	3	3	B.1.427	0.000151
ORF3a	41	L41F	Ctc	Ttc	3	3	B.1.556	0.022556
ORF3a	41	L41V	Ctc	Gtc	3	3	B.1.564.1	0.004732
ORF3a	41	L41H	cTc	cAc	3	3	B.1.595	0.000783
ORF3a	41	L41L	ctC	ctT	3	3	B.1.617.1	0.000387
ORF3a	41	L41I	Ctc	Atc	3	3	P.1	0.000047
ORF3a	41	L41F	Ctc	Ttc	3	3	P.1.1	0.000953
ORF3a	41	L41F	Ctc	Ttc	3	3	P.1.10	0.000808
ORF3a	41	L41F	Ctc	Ttc	3	3	P.1.4	0.00293
ORF3a	41	L41P	cTc	cCc	3	3	P.6	0.009434
ORF3a	41	L41del	CTC	---	3	3	U.3	0.011583
ORF3a	41	L41S	CTc	TCc	2	2		0.111111
ORF3a	41	L41L	ctC	ctT	2	2	AD.2	0.000438
ORF3a	41	L41S	CTc	TCc	2	2	All	0
ORF3a	41	L41L	ctC	ctT	2	2	AY.108	0.002205
ORF3a	41	L41F	Ctc	Ttc	2	2	AY.108	0.002205
ORF3a	41	L41R	cTc	cGc	2	2	AY.110	0.000225
ORF3a	41	L41R	cTc	cGc	2	2	AY.113	0.000285
ORF3a	41	L41P	cTc	cCc	2	2	AY.114	0.000462
ORF3a	41	L41L	ctC	ctT	2	2	AY.119	0.000071
ORF3a	41	L41del	CTC	---	2	2	AY.13	0.000322
ORF3a	41	L41F	Ctc	Ttc	2	2	AY.13	0.000322
ORF3a	41	L41F	Ctc	Ttc	2	2	AY.14	0.000176
ORF3a	41	L41F	Ctc	Ttc	2	2	AY.19	0.002281
ORF3a	41	L41del	CTC	---	2	2	AY.29	0.000032
ORF3a	41	L41R	cTc	cGc	2	2	AY.32	0.001065
ORF3a	41	L41F	Ctc	Ttc	2	2	AY.34	0.000194
ORF3a	41	L41R	cTc	cGc	2	2	AY.34.1	0.00102
ORF3a	41	L41F	Ctc	Ttc	2	2	AY.36	0.000296
ORF3a	41	L41I	Ctc	Atc	2	2	AY.38	0.000999
ORF3a	41	L41F	Ctc	Ttc	2	2	AY.38	0.000999
ORF3a	41	L41H	cTc	cAc	2	2	AY.39	0.000049
ORF3a	41	L41F	Ctc	Ttc	2	2	AY.4.2.1	0.000298
ORF3a	41	L41L	ctC	ctT	2	2	AY.42	0.00008
ORF3a	41	L41L	ctC	ctT	2	2	AY.46	0.000208
ORF3a	41	L41del	CTC	---	2	2	AY.46	0.000208
ORF3a	41	L41del	CTC	---	2	2	AY.46.2	0.001271
ORF3a	41	L41V	Ctc	Gtc	2	2	AY.47	0.000062
ORF3a	41	L41L	ctC	ctT	2	2	AY.47	0.000062
ORF3a	41	L41R	cTc	cGc	2	2	AY.5.3	0.000675
ORF3a	41	L41L	ctC	ctT	2	2	AY.5.3	0.000675
ORF3a	41	L41F	Ctc	Ttc	2	2	AY.5.4	0.000553
ORF3a	41	L41F	Ctc	Ttc	2	2	AY.58	0.001815
ORF3a	41	L41del	CTC	---	2	2	AY.6	0.000082
ORF3a	41	L41F	Ctc	Ttc	2	2	AY.60	0.001876
ORF3a	41	L41del	CTC	---	2	2	AY.67	0.000929
ORF3a	41	L41F	Ctc	Ttc	2	2	AY.69	0.000373
ORF3a	41	L41del	CTC	---	2	2	AY.75	0.000112
ORF3a	41	L41F	Ctc	Ttc	2	2	AY.75.1	0.000361
ORF3a	41	L41del	CTC	---	2	2	AY.81	0.003984
ORF3a	41	L41L	ctC	ctT	2	2	AY.82	0.002714
ORF3a	41	L41R	cTc	cGc	2	2	AY.84	0.000875
ORF3a	41	L41F	Ctc	Ttc	2	2	AY.85	0.000854
ORF3a	41	L41del	CTC	---	2	2	AY.9.2	0.000073
ORF3a	41	L41R	cTc	cGc	2	2	AY.91	0.001461
ORF3a	41	L41L	ctC	ctT	2	2	AY.98	0.000158
ORF3a	41	L41H	cTc	cAc	2	2	AY.98.1	0.000097
ORF3a	41	L41F	Ctc	Ttc	2	2	AY.99.2	0.000184
ORF3a	41	L41L	ctC	ctT	2	2	B.1.1.1	0.000653
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.1.174	0.006757
ORF3a	41	L41P	cTc	cCc	2	2	B.1.1.214	0.000111
ORF3a	41	L41I	Ctc	Atc	2	2	B.1.1.216	0.001781
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.1.231	0.006192
ORF3a	41	L41P	cTc	cCc	2	2	B.1.1.25	0.001137
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.1.27	0.011299
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.1.294	0.002532
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.1.322	0.017544
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.1.37	0.000386
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.1.370	0.025316
ORF3a	41	L41del	CTC	---	2	2	B.1.1.519	0.000079
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.1.55	0.025974
ORF3a	41	L41V	Ctc	Gtc	2	2	B.1.1.7	0.000002
ORF3a	41	L41R	cTc	cGc	2	2	B.1.1.7	0.000002
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.104	0.00738
ORF3a	41	L41del	CTC	---	2	2	B.1.160.33	0.00885
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.177.40	0.010309
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.177.52	0.003515
ORF3a	41	L41del	CTC	---	2	2	B.1.177.60	0.000437
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.177.60	0.000437
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.177.72	0.00678
ORF3a	41	L41L	ctC	ctT	2	2	B.1.221	0.000142
ORF3a	41	L41P	cTc	cCc	2	2	B.1.221.1	0.005814
ORF3a	41	L41P	cTc	cCc	2	2	B.1.232	0.001075
ORF3a	41	L41P	cTc	cCc	1	2	B.1.239	0.001221
ORF3a	41	L41P	cTC	cCT	1	2	B.1.239	0.001221
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.349	0.00143
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.351.2	0.000605
ORF3a	41	L41P	cTc	cCc	2	2	B.1.36	0.000292
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.36.29	0.001035
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.36.38	0.003284
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.362	0.003082
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.369	0.00057
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.436	0.002058
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.466.2	0.000782
ORF3a	41	L41del	CTC	---	2	2	B.1.471	0.005464
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.499	0.002101
ORF3a	41	L41I	Ctc	Atc	2	2	B.1.525	0.000226
ORF3a	41	L41del	CTC	---	2	2	B.1.525	0.000226
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.564	0.000852
ORF3a	41	L41L	ctC	ctT	2	2	B.1.565	0.001621
ORF3a	41	L41L	ctC	ctT	2	2	B.1.567	0.006667
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.595	0.000522
ORF3a	41	L41del	CTC	---	2	2	B.1.621	0.000177
ORF3a	41	L41P	cTc	cCc	2	2	B.1.621.1	0.001012
ORF3a	41	L41F	Ctc	Ttc	2	2	B.1.631	0.006734
ORF3a	41	L41P	cTc	cCc	2	2	C.37	0.000232
ORF3a	41	L41L	ctC	ctT	2	2	D.2	0.00015
ORF3a	41	L41del	CTC	---	2	2	D.2	0.00015
ORF3a	41	L41H	cTc	cAc	2	2	P.1	0.000032
ORF3a	41	L41L	ctC	ctT	2	2	P.1.12	0.000968
ORF3a	41	L41F	Ctc	Ttc	2	2	P.1.14	0.000096
ORF3a	41	L41L	ctC	ctT	2	2	P.1.15	0.000465
ORF3a	41	L41I	Ctc	Atc	2	2	P.1.15	0.000465
ORF3a	41	L41F	Ctc	Ttc	2	2	R.1	0.00018
ORF3a	41	L41Q	cTC	cAA	1	1	A	0.000387
ORF3a	41	L41H	cTc	cAc	1	1	A	0.000387
ORF3a	41	L41L	ctC	ctA	1	1	A	0.000387
ORF3a	41	L41F	Ctc	Ttc	1	1	A.1	0.000282
ORF3a	41	L41F	Ctc	Ttc	1	1	A.19	0.009434
ORF3a	41	L41P	cTc	cCc	1	1	A.2	0.000662
ORF3a	41	L41del	CTC	---	1	1	A.2.3	0.004739
ORF3a	41	L41H	cTc	cAc	1	1	A.2.5	0.000499
ORF3a	41	L41F	Ctc	Ttc	1	1	A.2.5.1	0.004808
ORF3a	41	L41F	Ctc	Ttc	1	1	AE.6	0.038462
ORF3a	41	L41del	CTC	---	1	1	AH.3	0.003802
ORF3a	41	L41del2	cTC	c--	1	1	All	0
ORF3a	41	L41Q	cTC	cAA	1	1	All	0
ORF3a	41	L41L	ctC	ctT	1	1	AY.1	0.000396
ORF3a	41	L41P	cTc	cCc	1	1	AY.10	0.00053
ORF3a	41	L41I	Ctc	Atc	1	1	AY.101	0.00049
ORF3a	41	L41R	cTc	cGc	1	1	AY.102	0.000027
ORF3a	41	L41I	Ctc	Atc	1	1	AY.102	0.000027
ORF3a	41	L41del	CTC	---	1	1	AY.102	0.000027
ORF3a	41	L41R	cTc	cGc	1	1	AY.104	0.001984
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.104	0.001984
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.105	0.000643
ORF3a	41	L41P	cTc	cCc	1	1	AY.106	0.000335
ORF3a	41	L41R	cTc	cGc	1	1	AY.108	0.001103
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.109	0.00074
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.11	0.001339
ORF3a	41	L41R	cTc	cGc	1	1	AY.11	0.001339
ORF3a	41	L41del	CTC	---	1	1	AY.111	0.000183
ORF3a	41	L41L	ctC	ctT	1	1	AY.113	0.000142
ORF3a	41	L41del	CTC	---	1	1	AY.113	0.000142
ORF3a	41	L41del	CTC	---	1	1	AY.114	0.000231
ORF3a	41	L41P	cTc	cCc	1	1	AY.116	0.000287
ORF3a	41	L41del	CTC	---	1	1	AY.117	0.000085
ORF3a	41	L41I	Ctc	Atc	1	1	AY.117	0.000085
ORF3a	41	L41L	ctC	ctT	1	1	AY.117	0.000085
ORF3a	41	L41del	CTC	---	1	1	AY.118	0.000063
ORF3a	41	L41I	Ctc	Atc	1	1	AY.119	0.000035
ORF3a	41	L41H	cTc	cAc	1	1	AY.119	0.000035
ORF3a	41	L41L	ctC	ctT	1	1	AY.12	0.000316
ORF3a	41	L41I	Ctc	Atc	1	1	AY.12	0.000316
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.12	0.000316
ORF3a	41	L41P	cTc	cCc	1	1	AY.120	0.000037
ORF3a	41	L41H	cTc	cAc	1	1	AY.120	0.000037
ORF3a	41	L41R	cTc	cGc	1	1	AY.120	0.000037
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.120.1	0.000321
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.120.2.1	0.000498
ORF3a	41	L41P	cTc	cCc	1	1	AY.121	0.000135
ORF3a	41	L41P	cTc	cCc	1	1	AY.14	0.000088
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.16	0.00038
ORF3a	41	L41R	cTc	cGc	1	1	AY.17	0.008197
ORF3a	41	L41L	ctC	ctT	1	1	AY.20	0.000039
ORF3a	41	L41R	cTc	cGc	1	1	AY.20	0.000039
ORF3a	41	L41del	CTC	---	1	1	AY.23	0.00007
ORF3a	41	L41H	cTc	cAc	1	1	AY.25	0.000006
ORF3a	41	L41I	Ctc	Atc	1	1	AY.26	0.000028
ORF3a	41	L41del	CTC	---	1	1	AY.28	0.00189
ORF3a	41	L41P	cTc	cCc	1	1	AY.29	0.000016
ORF3a	41	L41del	CTC	---	1	1	AY.29.1	0.000221
ORF3a	41	L41R	cTc	cGc	1	1	AY.3	0.00001
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.3.1	0.000085
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.30	0.000396
ORF3a	41	L41V	Ctc	Gtc	1	1	AY.30	0.000396
ORF3a	41	L41L	ctC	ctT	1	1	AY.32	0.000532
ORF3a	41	L41del	CTC	---	1	1	AY.33	0.000067
ORF3a	41	L41L	ctC	ctT	1	1	AY.34.1	0.00051
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.35	0.000233
ORF3a	41	L41L	ctC	ctT	1	1	AY.36	0.000148
ORF3a	41	L41I	Ctc	Atc	1	1	AY.36	0.000148
ORF3a	41	L41L	ctC	ctT	1	1	AY.37	0.000316
ORF3a	41	L41V	Ctc	Gtc	1	1	AY.39	0.000025
ORF3a	41	L41R	cTc	cGc	1	1	AY.4	0.000002
ORF3a	41	L41del1	Ctc	-tc	1	1	AY.4	0.000002
ORF3a	41	L41H	cTc	cAc	1	1	AY.4.2	0.000022
ORF3a	41	L41P	cTc	cCc	1	1	AY.4.2	0.000022
ORF3a	41	L41H	cTc	cAc	1	1	AY.4.4	0.000409
ORF3a	41	L41I	Ctc	Atc	1	1	AY.4.5	0.000107
ORF3a	41	L41del1	Ctc	-tc	1	1	AY.4.5	0.000107
ORF3a	41	L41L	ctC	ctT	1	1	AY.4.5	0.000107
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.41	0.000294
ORF3a	41	L41R	cTc	cGc	1	1	AY.42	0.00004
ORF3a	41	L41del	CTC	---	1	1	AY.42	0.00004
ORF3a	41	L41H	cTc	cAc	1	1	AY.42	0.00004
ORF3a	41	L41P	cTc	cCc	1	1	AY.45	0.000122
ORF3a	41	L41R	cTc	cGc	1	1	AY.45	0.000122
ORF3a	41	L41R	cTc	cGc	1	1	AY.46	0.000104
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.46.3	0.000934
ORF3a	41	L41P	cTc	cCc	1	1	AY.46.6	0.000072
ORF3a	41	L41R	cTc	cGc	1	1	AY.47	0.000031
ORF3a	41	L41del1	ctC	ct-	1	1	AY.48	0.000465
ORF3a	41	L41L	ctC	ctA	1	1	AY.49	0.003195
ORF3a	41	L41del	CTC	---	1	1	AY.5	0.000021
ORF3a	41	L41V	Ctc	Gtc	1	1	AY.5	0.000021
ORF3a	41	L41L	ctC	ctA	1	1	AY.52	0.000814
ORF3a	41	L41R	cTc	cGc	1	1	AY.52	0.000814
ORF3a	41	L41P	cTc	cCc	1	1	AY.54	0.000095
ORF3a	41	L41L	ctC	ctT	1	1	AY.55	0.000917
ORF3a	41	L41R	cTc	cGc	1	1	AY.57	0.000656
ORF3a	41	L41del	CTC	---	1	1	AY.59	0.00053
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.59	0.00053
ORF3a	41	L41L	ctC	ctT	1	1	AY.59	0.00053
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.6	0.000041
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.62	0.000436
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.63	0.000387
ORF3a	41	L41I	Ctc	Atc	1	1	AY.64	0.000595
ORF3a	41	L41del	CTC	---	1	1	AY.65	0.000533
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.67	0.000464
ORF3a	41	L41del	CTC	---	1	1	AY.7	0.000196
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.7.1	0.000113
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.70	0.000209
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.71	0.000475
ORF3a	41	L41del	CTC	---	1	1	AY.75.1	0.00018
ORF3a	41	L41P	cTc	cCc	1	1	AY.75.1	0.00018
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.76	0.004831
ORF3a	41	L41L	ctC	ctT	1	1	AY.77	0.001127
ORF3a	41	L41L	ctC	ctG	1	1	AY.84	0.000437
ORF3a	41	L41del	CTC	---	1	1	AY.84	0.000437
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.86	0.00083
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.88	0.000884
ORF3a	41	L41L	ctC	ctT	1	1	AY.9	0.000068
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.9	0.000068
ORF3a	41	L41I	Ctc	Atc	1	1	AY.9.1	0.000084
ORF3a	41	L41H	cTc	cAc	1	1	AY.9.1	0.000084
ORF3a	41	L41R	cTc	cGc	1	1	AY.9.2	0.000037
ORF3a	41	L41R	cTc	cGc	1	1	AY.90	0.000684
ORF3a	41	L41del	CTC	---	1	1	AY.90	0.000684
ORF3a	41	L41del	CTC	---	1	1	AY.91	0.00073
ORF3a	41	L41del	CTC	---	1	1	AY.93	0.000273
ORF3a	41	L41L	ctC	ctT	1	1	AY.93	0.000273
ORF3a	41	L41P	cTc	cCc	1	1	AY.98	0.000079
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.99	0.001049
ORF3a	41	L41I	Ctc	Atc	1	1	AY.99	0.001049
ORF3a	41	L41F	Ctc	Ttc	1	1	AY.99.1	0.001553
ORF3a	41	L41R	cTc	cGc	1	1	AY.99.1	0.001553
ORF3a	41	L41del	CTC	---	1	1	AY.99.2	0.000092
ORF3a	41	L41P	cTc	cCc	1	1	AZ.3	0.00152
ORF3a	41	L41del	CTC	---	1	1	B	0.000128
ORF3a	41	L41L	ctC	ctT	1	1	B	0.000128
ORF3a	41	L41R	cTc	cGc	1	1	B	0.000128
ORF3a	41	L41V	Ctc	Gtc	1	1	B.1	0.000009
ORF3a	41	L41H	cTc	cAc	1	1	B.1.1	0.000018
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.1.1	0.000327
ORF3a	41	L41I	Ctc	Atc	1	1	B.1.1.101	0.01
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.1.135	0.004695
ORF3a	41	L41I	Ctc	Atc	1	1	B.1.1.139	0.022727
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.1.160	0.02381
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.1.163	0.007634
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.1.170	0.001247
ORF3a	41	L41P	cTc	cCc	1	1	B.1.1.189	0.001513
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.1.216	0.00089
ORF3a	41	L41del	CTC	---	1	1	B.1.1.222	0.000204
ORF3a	41	L41del	CTC	---	1	1	B.1.1.225	0.007194
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.1.241	0.00207
ORF3a	41	L41L	ctC	ctT	1	1	B.1.1.253	0.002506
ORF3a	41	L41del	CTC	---	1	1	B.1.1.28	0.000311
ORF3a	41	L41H	cTc	cAc	1	1	B.1.1.28	0.000311
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.1.291	0.000742
ORF3a	41	L41P	cTc	cCc	1	1	B.1.1.306	0.000438
ORF3a	41	L41I	Ctc	Atc	1	1	B.1.1.306	0.000438
ORF3a	41	L41L	ctC	ctT	1	1	B.1.1.310	0.015152
ORF3a	41	L41P	cTc	cCc	1	1	B.1.1.317	0.000412
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.1.318	0.000302
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.1.326	0.001761
ORF3a	41	L41L	ctC	ctT	1	1	B.1.1.33	0.000421
ORF3a	41	L41del	CTC	---	1	1	B.1.1.33	0.000421
ORF3a	41	L41V	Ctc	Gtc	1	1	B.1.1.33	0.000421
ORF3a	41	L41L	ctC	ctT	1	1	B.1.1.34	0.013158
ORF3a	41	L41L	ctC	ctT	1	1	B.1.1.343	0.020833
ORF3a	41	L41L	ctC	ctT	1	1	B.1.1.37	0.000193
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.1.385	0.004464
ORF3a	41	L41del	CTC	---	1	1	B.1.1.39	0.00051
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.1.398	0.003226
ORF3a	41	L41del	CTC	---	1	1	B.1.1.409	0.002833
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.1.434	0.000349
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.1.463	0.0625
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.1.50	0.000679
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.1.513	0.012346
ORF3a	41	L41I	Ctc	Atc	1	1	B.1.1.519	0.00004
ORF3a	41	L41P	cTc	cCc	1	1	B.1.1.519	0.00004
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.1.522	0.017241
ORF3a	41	L41del1	cTc	c-c	1	1	B.1.1.7	0.000001
ORF3a	41	L41P	cTc	cCc	1	1	B.1.111	0.001175
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.126	0.001276
ORF3a	41	L41del	CTC	---	1	1	B.1.160	0.000031
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.160.14	0.002119
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.160.7	0.002079
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.162	0.005025
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.170	0.00431
ORF3a	41	L41V	Ctc	Gtc	1	1	B.1.177	0.000013
ORF3a	41	L41I	Ctc	Atc	1	1	B.1.177	0.000013
ORF3a	41	L41L	ctC	ctT	1	1	B.1.177.10	0.000878
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.177.18	0.00116
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.177.33	0.001645
ORF3a	41	L41R	cTc	cGc	1	1	B.1.177.44	0.000519
ORF3a	41	L41L	ctC	ctT	1	1	B.1.177.56	0.000668
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.177.57	0.000281
ORF3a	41	L41del	CTC	---	1	1	B.1.177.6	0.000977
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.177.69	0.001484
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.177.73	0.000566
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.177.83	0.001481
ORF3a	41	L41R	cTc	cGc	1	1	B.1.2	0.000009
ORF3a	41	L41H	cTc	cAc	1	1	B.1.2	0.000009
ORF3a	41	L41del2	cTC	c--	1	1	B.1.2	0.000009
ORF3a	41	L41I	Ctc	Atc	1	1	B.1.206	0.000816
ORF3a	41	L41P	cTc	cCc	1	1	B.1.210	0.002132
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.214.2	0.0006
ORF3a	41	L41del	CTC	---	1	1	B.1.221	0.000071
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.232	0.000537
ORF3a	41	L41L	ctC	ctT	1	1	B.1.234	0.000132
ORF3a	41	L41L	ctC	ctT	1	1	B.1.239	0.001221
ORF3a	41	L41del	CTC	---	1	1	B.1.241	0.000812
ORF3a	41	L41P	cTc	cCc	1	1	B.1.243	0.00007
ORF3a	41	L41L	ctC	ctT	1	1	B.1.258.17	0.000104
ORF3a	41	L41P	cTc	cCc	1	1	B.1.265	0.001271
ORF3a	41	L41P	cTc	cCc	1	1	B.1.279	0.000514
ORF3a	41	L41I	Ctc	Atc	1	1	B.1.320	0.001245
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.326	0.007576
ORF3a	41	L41L	ctC	ctT	1	1	B.1.350	0.002933
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.355	0.011111
ORF3a	41	L41H	cTc	cAc	1	1	B.1.36	0.000146
ORF3a	41	L41P	cTc	cCc	1	1	B.1.36.18	0.00042
ORF3a	41	L41P	cTc	cCc	1	1	B.1.36.29	0.000517
ORF3a	41	L41L	ctC	ctT	1	1	B.1.36.36	0.000602
ORF3a	41	L41I	Ctc	Atc	1	1	B.1.36.8	0.001
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.361	0.001289
ORF3a	41	L41L	ctC	ctT	1	1	B.1.361	0.001289
ORF3a	41	L41L	ctC	ctT	1	1	B.1.396	0.000706
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.422	0.000812
ORF3a	41	L41P	cTc	cCc	1	1	B.1.425	0.002994
ORF3a	41	L41R	cTc	cGc	1	1	B.1.427	0.00005
ORF3a	41	L41L	ctC	ctT	1	1	B.1.427	0.00005
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.428.3	0.012821
ORF3a	41	L41V	Ctc	Gtc	1	1	B.1.429	0.000024
ORF3a	41	L41L	ctC	ctT	1	1	B.1.436	0.001029
ORF3a	41	L41I	Ctc	Atc	1	1	B.1.436	0.001029
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.456	0.003268
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.459	0.004082
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.480	0.002488
ORF3a	41	L41L	ctC	ctT	1	1	B.1.499	0.00105
ORF3a	41	L41P	cTc	cCc	1	1	B.1.517	0.000427
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.543	0.01
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.544	0.006024
ORF3a	41	L41P	cTc	cCc	1	1	B.1.561	0.000397
ORF3a	41	L41del	CTC	---	1	1	B.1.563	0.016949
ORF3a	41	L41I	Ctc	Atc	1	1	B.1.577	0.000687
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.577	0.000687
ORF3a	41	L41P	cTc	cCc	1	1	B.1.580	0.004065
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.587	0.001898
ORF3a	41	L41L	ctC	ctT	1	1	B.1.593	0.01087
ORF3a	41	L41I	Ctc	Atc	1	1	B.1.595	0.000261
ORF3a	41	L41L	ctC	ctT	1	1	B.1.595.3	0.026316
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.602	0.006536
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.605	0.005952
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.611	0.04
ORF3a	41	L41P	cTc	cCc	1	1	B.1.619	0.000871
ORF3a	41	L41I	Ctc	Atc	1	1	B.1.619.1	0.000641
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.620	0.000946
ORF3a	41	L41P	cTc	cCc	1	1	B.1.621	0.000089
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.627	0.00202
ORF3a	41	L41L	ctC	ctG	1	1	B.1.630	0.005236
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.637	0.000073
ORF3a	41	L41del	CTC	---	1	1	B.1.637	0.000073
ORF3a	41	L41del	CTC	---	1	1	B.1.638	0.052632
ORF3a	41	L41F	Ctc	Ttc	1	1	B.1.88.1	0.004808
ORF3a	41	L41L	ctC	ctA	1	1	B.23	0.002924
ORF3a	41	L41P	cTc	cCc	1	1	B.40	0.000364
ORF3a	41	L41L	ctC	ctT	1	1	B.6.6	0.000889
ORF3a	41	L41F	Ctc	Ttc	1	1	B.6.6	0.000889
ORF3a	41	L41L	ctC	ctT	1	1	C.14	0.004329
ORF3a	41	L41F	Ctc	Ttc	1	1	C.36	0.000911
ORF3a	41	L41L	ctC	ctT	1	1	C.36	0.000911
ORF3a	41	L41P	cTc	cCc	1	1	C.36.3	0.000567
ORF3a	41	L41I	Ctc	Atc	1	1	C.37	0.000116
ORF3a	41	L41del	CTC	---	1	1	C.37	0.000116
ORF3a	41	L41P	cTc	cCc	1	1	D.2	0.000075
ORF3a	41	L41I	Ctc	Atc	1	1	M.3	0.076923
ORF3a	41	L41F	Ctc	Ttc	1	1	N.4	0.004255
ORF3a	41	L41F	Ctc	Ttc	1	1	N.5	0.001767
ORF3a	41	L41del	CTC	---	1	1	P.1.14	0.000048
ORF3a	41	L41del	CTC	---	1	1	P.1.15	0.000232
ORF3a	41	L41del	CTC	---	1	1	P.1.16	0.000374
ORF3a	41	L41F	Ctc	Ttc	1	1	P.1.6	0.001946
ORF3a	41	L41L	ctC	ctT	1	1	P.1.7	0.000319
ORF3a	41	L41L	ctC	ctT	1	1	P.2	0.000187
ORF3a	41	L41F	Ctc	Ttc	1	1	P.3	0.001595
ORF3a	41	L41P	cTc	cCc	1	1	Q.1	0.000126
ORF3a	41	L41F	Ctc	Ttc	1	1	Q.3	0.000145
ORF3a	41	L41L	ctC	ctT	1	1	Q.8	0.000165
ORF3a	41	L41P	cTc	cCc	1	1	R.1	0.00009

CoV-GLUE is still in development. CoV-GLUE was originally developed as part of COG-UK by Josh Singer using the GLUE framework at the MRC-University of Glasgow Centre for Virus Research (CVR). In 2021 it was redeveloped by Richard Orton to scale to the millions of genome sequences available. We acknowledge support from the MRC (MC_UU_12014/12), WT (220977/Z/20/Z) and UKRI G2P (MR/W005611/1). Please contact Richard Orton with any queries: Richard.Orton@glasgow.ac.uk

CoV-GLUE uses sequence data from GISAID. GISAID data provided via this web application is subject to GISAID's Terms and Conditions.